[gmx-users] Methanol geometry parameters

[Vitaly V. Chaban]

You, perhaps, need to care about *compatibility* of this old methanol and
your solute molecule.





On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <peter.stern at weizmann.ac.il>
wrote:

> The force field parameters are defined in ffbonded.itp and ffnonbonded.itp.
> You still need starting coordinates for your molecule.
> There are plenty of programs which will do this, but you can probably find
> it in some pdb entry.
> But, it is also trivial to do by hand since there are only two atoms and
> you know the C-O bond distance, e.g.:
> HETATM    1  C   MOH  1  1       0.000   0.000   1.410  1.00  1.00
> HETATM    2  O  MOH  1  1       0.000   0.000   0.000  1.00  1.00
>
> You should use an existing pdb or gro file as a template for the correct
> format.  gmx pdb2gmx will add the H-atoms.
>
> Peter Stern
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Daniele
> Veclani
> Sent: Thursday, December 03, 2015 3:31 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Methanol geometry parameters
>
> Thank you for your reply.
>
> Yes, The .itp file for methanol comes from gromacs. But but I need the
> .gro file. I need the geometric parameters like distances, angles and
> diedrals.
> these parameters are not in the .itp file or I'm wrong??
>
> Best regards
> D.V.
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